Contacts of the strand formed by residues 127 - 132 (chain F) in PDB entry 1H48
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 127 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53E ALA* 4.5 3.4 - - - +
91F LEU* 5.1 0.9 - - + -
94F VAL* 3.8 13.5 - - + -
96F VAL* 5.9 0.2 - - + -
113F ARG* 2.9 47.7 + - + +
116F ILE* 3.7 44.4 - - + -
117F ALA* 4.1 7.2 - - + +
122F CYS* 3.7 25.1 - - - -
123F HIS 4.2 3.1 - - - +
124F MET 3.0 10.4 + - - +
125F ASP 3.2 1.4 + - - -
126F ASP* 1.3 85.1 - - - +
128F ASN* 1.3 63.6 + - - +
129F VAL* 4.3 4.5 - - + -
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Residues in contact with ASN 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E ARG* 5.9 0.6 - - - +
50E GLY* 3.4 23.8 - - - +
53E ALA* 3.1 18.5 - - + -
55E GLY* 3.1 41.6 + - - -
94F VAL 3.0 10.8 + - - +
95F ASP* 2.9 25.7 + - - +
96F VAL* 2.8 26.0 + - - +
113F ARG* 4.6 3.8 - - - +
127F VAL* 1.3 75.5 - - - +
129F VAL* 1.3 87.7 + - - +
130F LYS* 3.9 3.0 - - - +
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Residues in contact with VAL 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E GLY* 4.5 8.1 - - - -
56E ASP* 5.0 0.2 - - - +
40F ALA* 6.2 0.2 - - + -
96F VAL* 3.6 18.4 - - + -
98F ILE* 3.7 28.5 - - + -
109F ILE* 3.7 39.0 - - + +
112F MET* 4.0 11.2 - - + -
113F ARG* 4.2 18.6 - - + +
116F ILE* 4.1 26.0 - - + -
127F VAL* 4.3 3.1 + - + -
128F ASN* 1.3 87.7 + - - +
130F LYS* 1.3 67.3 + - - +
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Residues in contact with LYS 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E HIS* 2.7 20.3 + - - +
6E GLY* 5.2 0.7 - - - -
46E ASP* 3.6 41.3 - - + +
50E GLY* 4.1 0.9 - - - -
55E GLY 4.0 4.7 - - - +
56E ASP* 3.3 25.1 - - + +
95F ASP* 2.6 40.7 + - - -
96F VAL 2.9 11.5 + - - +
97F THR* 2.8 31.2 + - + +
98F ILE* 2.9 28.1 + - - +
109F ILE* 4.1 7.0 - - - -
128F ASN* 3.9 5.6 - - - +
129F VAL* 1.3 76.4 - - - +
131F ALA* 1.3 62.8 + - - +
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Residues in contact with ALA 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E ASP* 5.4 1.4 - - - +
56E ASP* 3.2 10.9 + - - +
97F THR* 5.3 0.9 - - - -
98F ILE* 3.3 11.7 - - + +
105F MET* 3.7 31.6 - - + -
109F ILE* 4.2 3.1 - - + +
130F LYS* 1.3 79.6 - - - +
132F THR* 1.3 63.5 + - - +
901F C5P 3.1 47.1 + - + +
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Residues in contact with THR 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E PHE* 3.7 38.0 + - + +
8E ASP* 4.2 8.2 + - - -
46E ASP* 5.2 6.7 - - - -
97F THR* 4.5 6.7 - - + -
98F ILE 2.9 12.0 + - - +
99F ILE* 3.4 9.5 - - + -
100F ALA 3.1 24.6 + - - +
130F LYS* 6.4 0.2 - - - -
131F ALA* 1.3 76.0 - - - +
133F THR* 1.3 74.4 + - - +
901F C5P 2.7 37.3 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il